The most comprehensive study ever conducted into inequality in Britain has revealed a country in which boys struggle academically, disabled children face shocking levels of bullying and progress towards pay equality for women has stalled.

How Fair is Britain?, a definitive 700-page report from the Equality and Human Rights Commission on discrimination and disadvantage in British society, charts inequalities from birth, through education, into the workplace and on to retirement.

Trevor Phillips, chairman of the EHRC, said the study revealed that while British attitudes towards issues of race, gender and sexuality are now "light years" ahead of previous generations, the reality on the ground has yet to fully catch up. In consequence, there are deep divisions in Britain's classrooms, different experiences of the criminal justice system and a stubbornly large pay gap between men and women. In full-time work, women are still paid 16.4% less than men, a figure that rises to 55% in the finance sector.

Phillips will say tomorrow, when the report is launched, that despite the progress made, Britain is a country where long-standing inequalities are unresolved and where new social and economic fault lines are now emerging.

In publishing the report, the equality body is laying down a challenge to the coalition government, warning that the economic outlook and public service reforms are "major risk factors" in progress towards a fairer society.

In his speech, Phillips will declare: "It is not the commission's role to advise on economic policy. But it is our role to ensure that whatever is done is done fairly." Already the body has written to the Treasury warning that it must take account of the impact of policy decisions on groups who could be disadvantaged. Campaigners and Labour have accused the government of making women bear the brunt of the spending cuts announced in June's emergency budget.

Phillips will also highlight how complicated the issue of equalities has become. "Inequality and disadvantage don't come neatly packaged in parcels marked age, or disability, or gender, or race. They emerge often as a subset of a strand – not as a disability issue, but as a mental health issue; not as a generalised ethnic penalty, but as a result of being Pakistani; not a pay gap for working women, but a pay gap for working mothers," he will say.

The study will also reveal the deep injustices faced by young people of certain ethnicities by showing how much more likely they are to be stopped and searched by police. And it will highlight a shocking disparity between the child mortality rates for black and white babies.

In a chapter on education seen exclusively by the Observer, the study highlights a growing gender gap at school that is seeing boys slip behind at the age of five, underperform at GCSE and enter university in lower numbers.

It also reaffirms concerns about class divides, showing once again that children born into disadvantaged families face a long, uphill struggle that too often ends in lower life chances. And it reveals that four out of five children with special educational needs have been bullied.

Phillips will argue that fairness is not just a measure of equality – whether of opportunity or outcome. "It involves a judgment, based on objective data, as to whether what is being done is reasonable and proportionate in the circumstances, and that sometimes means treating some people differently," he will say, adding: "To coin a phrase – when it comes to addressing inequality and unfairness, we really are all in it together."

Money cannot always buy people fairness, he will add, giving the example of a billionaire in a wheelchair who cannot get into a restaurant because there is no ramp.

Campaigners on gender, race, disability and other issues have welcomed the report. Andy Burnham, the new shadow education secretary, said he wanted fairness to be at the heart of his role. He argued that too often the postcode a child is born in determines where he or she ends up. Burnham spoke specifically of the way that young people from deprived backgrounds are frozen out of top jobs because they are not well enough connected, or rich enough, to accept unpaid internships – a culture that has spread from the media to every part of the workplace.

Women's rights groups, meanwhile, will jump on the issue of equal pay. Ceri Goddard, chief executive of the women's rights group the Fawcett Society, said closing the gap required much "greater political will" than had been apparent for years.